title: "Global Meta-analysis"
output:
html_document:
toc: false
toc_float: false
code_folding: hide
number_sections: true
theme: spacelab
---
## MA_HC_Excitadoras_F {.tabset .tabset-pills -}
```r
library(dplyr)
library(knitr)
library(DT)
library(ggplot2)
library(plotly)
load("/clinicfs/projects/i63/tfm_hipocampo/Metaanalysis_HC/HC/Excitadoras/F/MA_HC_Excitadoras_F.RData")
```
### MA results (significant genes) {-}
datatable(sig.genes.df[,c(1:5,12,15)], caption='Statistics of 1588 significant genes',rownames=FALSE, escape = FALSE, filter = 'top')
MA results (volcano plot)
ggplotly(volcano_plot)
Individual results (summary)
kable(table_sum, col.names = c('Study','All genes','Significant genes'))
| Study43 |
11135 |
6391 |
| GSE163577 |
21025 |
361 |
| syn52293442_hc |
18543 |
4543 |
sessionInfo
date()
## [1] "Sun May 25 16:04:11 2025"
sessionInfo()
## R version 4.2.2 (2022-10-31)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: CentOS Linux 7 (Core)
##
## Matrix products: default
## BLAS/LAPACK: /opt/sci-soft/software/FlexiBLAS/3.0.4-GCC-11.2.0/lib64/libflexiblas.so.3.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] plotly_4.10.4 DT_0.26 knitr_1.41 ggplot2_3.5.2 dplyr_1.0.10 limma_3.54.0
## [7] tibble_3.1.8 metafor_3.8-1 metadat_1.2-0 Matrix_1.5-3 Biobase_2.58.0 BiocGenerics_0.44.0
##
## loaded via a namespace (and not attached):
## [1] tidyselect_1.2.0 xfun_0.35 bslib_0.4.2 purrr_0.3.5 lattice_0.20-45 vctrs_0.6.5
## [7] generics_0.1.3 htmltools_0.5.4 viridisLite_0.4.1 yaml_2.3.6 utf8_1.2.2 rlang_1.1.6
## [13] pillar_1.8.1 jquerylib_0.1.4 glue_1.6.2 withr_2.5.0 DBI_1.1.3 RColorBrewer_1.1-3
## [19] lifecycle_1.0.3 stringr_1.5.0 gtable_0.3.1 htmlwidgets_1.6.0 evaluate_0.19 labeling_0.4.2
## [25] fastmap_1.1.0 crosstalk_1.2.0 fansi_1.0.3 highr_0.9 scales_1.4.0 cachem_1.0.6
## [31] jsonlite_1.8.4 farver_2.1.1 png_0.1-8 digest_0.6.31 stringi_1.7.8 grid_4.2.2
## [37] mathjaxr_1.6-0 cli_3.4.1 tools_4.2.2 magrittr_2.0.3 sass_0.4.4 lazyeval_0.2.2
## [43] dichromat_2.0-0.1 tidyr_1.2.1 pkgconfig_2.0.3 ellipsis_0.3.2 data.table_1.14.6 assertthat_0.2.1
## [49] rmarkdown_2.19 httr_1.4.4 rstudioapi_0.14 R6_2.5.1 nlme_3.1-161 compiler_4.2.2